Short-Term Metabolome Dynamics and Carbon, Electron, and ATP Balances in Chemostat-Grown Saccharomyces cerevisiae CEN.PK 113-7D following a Glucose Pulse

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O₂ uptake and CO₂ evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO₂ evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.     

Effect of bacterial density and substrate concentration on yield coefficients.

Measurements were made of the yield coefficient during the aerobic metabolism of glucose by a heterogeneous bacterial mixture. Expressed in terms of carbon, the coefficient was approximately 0.48. The value did not vary with initial bacterial densities ranging from 0.4 pg to 40 micrograms of cell carbon per ml and with glucose concentrations ranging from 43 pg to 100 micrograms of carbon per ml. Under all these circumstances, about 44% of the glucose carbon was converted to CO2, and 7.4% was excreted as organic products. The significance of uncharacterized organic substrates contaminating the medium to the coefficients calculated for low glucose concentrations is discussed.     

Production of nadh by microbial reduction of added nad

Summary Of thirteen bacterial strains and four strains of yeast-like organisms, permeabilized cells of two bacterial and one yeast strain effectively converted added NAD⁺ into NADH in the presence of glucose as substrate.Arthrobacter ureafaciens reduced more than 90% of 10 mM NAD⁺ into NADH during 1h.     

Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors

Metabolism of living cells converts substrates into metabolic energy, redox potential and metabolic end products that are essential to maintain cellular function. The flux distribution among the various biochemical pathways is determined by the kinetic properties of enzymes which are subject to strict regulatory control. Simulation of metabolic behavior therefore requires the complete knowledge of biochemical pathways, enzyme kinetics as well as their regulation. Unfortunately, complete kinetic and regulatory information is not available for microbial cells, thus preventing accurate dynamic simulation of their metabolic behavior. However, it is possible to define wider limits on metabolic behavior based solely on flux balances of biochemical pathways. We present here comprehensive information about the catabolic pathways of the bacterium Escherichia coli. Using this biochemical database, we formulate a stoichiometric model of the bacterial network of fueling reactions. After logical structural reduction, the network consists of 53 metabolic fluxes and 30 metabolites. The solution space of this under-determined system of equations presents the bounds of metabolic flux distribution that the bacterial cell can achieve. We use specific objective functions and linear optimization to investigate the capability of E. coli catabolism to maximally produce the 12 biosynthetic precursors and three key cofactors within this solution space. For the three cofactors, the maximum yields are calculated to be 18.67 ATP, 11.6 NADH and 11 NADPH per glucose molecule, respectively. The yields of NADH and NADPH are less than 12 owing to the energy costs of importing glucose. These constraints are made explicit by the interpretation of shadow prices. The optimal yields of the 12 biosynthetic precursors are computed. Four of the 12 precursors (3-phosphoglycerate, phosphoenolpyruvate, pyruvate and oxaloacetate) can be made by E. coli with complete carbon conversion. Conversely, none of the sugar monophosphates can be made with 100% carbon conversion and analysis of the shadow prices reveals that this conversion is constrained by the energy cost of importing glucose. Three of the 12 precursors (acetyl-coA, α-ketoglutarate, and succinyl-coA) cannot be made with full carbon conversion owing to stoichiometric constraints; there is no route to these compounds without carrying out a decarboxylation reaction. Metabolite flux balances and linear optimization have thus been used to determine the catabolic capabilities of E. coli .     

Metabolism of organic acids by Thiobacillus neapolitanus

Summary A comparative study has been made of the metabolism in several strains of Thiobacillus neapolitanus of formate, acetate, propionate, butyrate, valerate and pyruvate. Conflicting reports in the literature concerning the mechanism of pyruvate assimilation in thiobacilli have been resolved. Pyruvate undergoes decarboxylation to yield acetyl coenzyme A, which is converted to glutamate, proline and arginine via reactions of the incomplete Krebs' cycle of this organism. Pyruvate is converted also to alanine, valine, isoleucine, leucine and lysine by mechanisms like those in heterotrophs. No aspartate is formed from the C-3 of pyruvate. Removal of the C-1 of pyruvate yields carbon dioxide, which is refixed into all cell constituents. Formate is not produced by this scission reaction, as formate itself is incorporated almost exclusively into purines. Aspartate can be synthesized by the activities of phosphoenolpyruvate carboxylase and oxaloacetate-glutamate transamination. Carbon from propionate is converted principally to lipids, although some amino acid production occurs with the same distinctive labelling pattern as is found after acetate assimilation by T. neapolitanus strains C and X. Butyrate and valerate also showed some distinctive patterns of incorporation into cell constituents. Fluoropyruvate and fluoropropionate inhibited the growth of T. neapolitanus and the mechanisms of this poisoning are discussed.Generally these compounds contributed only small proportions of the total cell carbon and tended to be converted to limited numbers of cell components. The thiobacilli thus tend to conserve carbon from these compounds and not to degrade them to carbon dioxide on a large scale when growing in an otherwise autotrophic medium.     

Lithotrophic growth ofSulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia

Sulfurospirillum deleyianum grew in batch culture under anoxic conditions with sulfide (up to 5 mM) as electron donor, nitrate as electron acceptor, and acetate as carbon source. Nitrate was reduced to ammonia via nitrite, a quantitatively liberated intermediate. Four moles of sulfide were oxidized to elemental sulfur per mole nitrate converted to ammonia. The molar growth yield per mole sulfide consumed, Y_m, was 1.5 ± 0.2 g mol^–1 for the reduction of nitrate to ammonia. By this type of metabolism, S. deleyianum connected the biogeochemical cycles of sulfur and nitrogen. The sulfur reductase activity in S. deleyianum was inducible, as the activity depended on the presence of sulfide or elemental sulfur during cultivation with nitrate or fumarate as electron acceptor. Hydrogenase activity was always high, indicating that the enzyme is constitutively expressed. The ammonia-forming nitrite reductase was an inducible enzyme, expressed when cells were cultivated with nitrate, nitrite, or elemental sulfur, but repressed after cultivation with fumarate. Received: 13 March 1995 / Accepted: 29 May 1995     

Modification of yeast metabolism by immobilization onto porous glass

Summary Porous glass beads are used to immobilizeSaccharomyces carlsbergensis cells. If silica pores are large enough, adsorption occurs. On the other hand, activation of the silica by glutaraldehyde allows the cells to bind onto the support. In the other case, the most porous glass has the greatest retention capacities. In all cases, 15 min is sufficient for support saturation by microorganisms.The study of glucose fermentation in immobilized cells shows that immobilization modifies the metabolism. Adsorption leads to an acceleration of metabolism, while a slowing down of the cell's activity follows covalent binding. Nevertheless, in both cases yield of glucose converted into ethanol increases while yield of glucose converted into carbon dioxide decreases.     

Dynamic mechanistic modeling of the multienzymatic one‐pot reduction of dehydrocholic acid to 12‐keto ursodeoxycholic acid with competing substrates and cofactors

Ursodeoxycholic acid (UDCA) is a bile acid which is used as pharmaceutical for the treatment of several diseases, such as cholesterol gallstones, primary sclerosing cholangitis or primary biliary cirrhosis. A potential chemoenzymatic synthesis route of UDCA comprises the two‐step reduction of dehydrocholic acid to 12‐keto‐ursodeoxycholic acid (12‐keto‐UDCA), which can be conducted in a multienzymatic one‐pot process using 3α‐hydroxysteroid dehydrogenase (3α‐HSDH), 7β‐hydroxysteroid dehydrogenase (7β‐HSDH), and glucose dehydrogenase (GDH) with glucose as cosubstrate for the regeneration of cofactor. Here, we present a dynamic mechanistic model of this one‐pot reduction which involves three enzymes, four different bile acids, and two different cofactors, each with different oxidation states. In addition, every enzyme faces two competing substrates, whereas each bile acid and cofactor is formed or converted by two different enzymes. First, the kinetic mechanisms of both HSDH were identified to follow an ordered bi–bi mechanism with EBQ‐type uncompetitive substrate inhibition. Rate equations were then derived for this mechanism and for mechanisms describing competing substrates. After the estimation of the model parameters of each enzyme independently by progress curve analyses, the full process model of a simple batch‐process was established by coupling rate equations and mass balances. Validation experiments of the one‐pot multienzymatic batch process revealed high prediction accuracy of the process model and a model analysis offered important insight to the identification of optimum reaction conditions. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:375–386, 2015     

Analysis of glucose carbon fluxes in continuous cultures of Bacillus thuringiensis

 The glucose carbon fluxes in continuous cultures of Bacillus thuringiensis grown in a complex medium have been studied as a function of the growth rate. The results are discussed in the light of a growth model. From reduced nicotinamide adenine dinucleotide (NADH) and carbon balances it was determined that the fraction of glucose consumed for biomass synthesis decreased with the growth rate, while the glucose flux through the tricarboxylic acid (TCA) cycle diminished after a threshold value of D=0.34 h^-1, where D=dilution rate. At the highest growth rate tested, glucose was used almost exclusively as the energy source, via fermentative pathways, which indicates that the yeast extract was used as the carbon source. The specific rate of oxygen consumption increased with growth even after the beginning of the accumulation of acids, indicating that the respiratory chain was not saturated. The results suggest that there is a mismatch between glycolysis and TCA cycle capacity, depending on the growth rate. Furthermore, values of (P/O) ratio and m _ATP are presented, where (P/O) is mole of ATP formed per gram atom oxygen consumed by the respiratory chains and m _ATP is the maintenance requirement for ATP. Received: 6 September 1995/Received last revision: 13 February 1996/Accepted: 20 February 1996     

Clostridium magnum sp. nov., a non-autotrophic homoacetogenic bacterium

A new mesophilic, sporeforming, strictly anaerboic bacterium was isolated form enrichments with 2,3-butanediol as sole substrate and pasteurized freshwater sediment as inoculum. Cells were large, motile rods, and elliptical spores were formed subterminally or centrally. They stained Gram-negative, but no typical outer membrane layer could be observed by electron microscopy of ultrathin sections. 2,3-Butanediol, acetoin, fructose, glucose, sucrose, xylose, malate and citrate served as substrates and were completely converted to acetate with concomitant reduction of carbon dioxide. Growth on glucose (t _dmin=1.4 h) was faster than on butanediol (t _dmin=3.6 h). No growth occurred on hydrogen/carbon dioxide, on formate or on methanol. The guanine plus cytosine content of the DNA was 29.1%. The new isolate is described as a new species, Clostridium magnum sp. nov.     

Evidence in vivo that most of the intraluminally absorbed glucose is absorbed intact into the portal vein and not metabolized to lactate.

Studies in vitro and acute studies in vivo have indicated that the intestine may be a significant producer of portal-venous lactate, a major carbon source for liver glycogen synthesis. To determine if a significant portion of intraluminal glucose is converted into lactate by the intestine in vivo, we measured the ratio of intraluminal glucose which is absorbed intact into the portal vein to that which is converted into lactate by the intestine in a chronically catheterized rat, in which catheters were surgically placed into the portal vein, aorta and stomach. This ratio was 36-42 when intraluminal [U-14C]glucose concentrations of 5-200 mM were used, suggesting that the intestine may not be a significant source of portal-venous lactate in vivo. Under hypoxic conditions [PaO2 less than 40 Torr (5.3 kPa)] the ratio decreased to 2.1, indicating that the amount of intraluminal glucose converted into lactate had increased significantly.     

ATP formation associated with fumarate and nitrate reduction in growing cultures of Veillonella alcalescens

Molar growth yields, fermentation balances and enzyme activities were measured in Veillonella alcalescens grown anaerobically with different substrates in the absence or presence of fumarate or nitrate. The molar growth yields on malate (14.3 g dry wt bacteria/mole substrate) and citrate (19.3) were higher than that on lactate (8.6). The molar growth yield on lactate was increased to 15.5 or 19.8 by the addition of fumarate or nitrate, respectively, to the growth medium, and the molar growth yield on citrate was increased to 25.3 by addition of nitrate. Active growth yield was 25.5. From fermentation balances and fermentation systems similar Y_ATP values (g dry wt bacteria/mole ATP) were calculated for all substrates or mixtures of substrates assuming that one mole of ATP is generated at the electron transport from pyruvate, NADH and NADPH to nitrate or fumarate whereas ATP is not produced in the electron transport from lactate to fumarate or nitrate, and, therefore, this assumption was considered to reflect the actual situation. The mean Y_ATP value at a doubling time of 1 h was 16.5 g dry wt bacteria/mole ATP for growth without an added hydrogen acceptor, 14.4 for growth with fumarate, and 14.2 for growth with nitrate.     

Aerobic degradation of pyridine by a new bacterial strain, <Emphasis Type="Italic">Shinella zoogloeoides</Emphasis> BC026

A new bacterial strain, Shinella zoogloeoides BC026, which utilizes pyridine as its sole carbon, nitrogen and energy source, was isolated from the activated sludge of a coking wastewater treatment plant. The BC026 strain completely degraded up to 1,806 mg/l of pyridine in 45.5 h. The optimum degradation conditions were pH 8.0 and temperature 30–35°C. According to product monitoring and genetic analysis, the pyridine ring was cleaved between C₂ and N, resulting in 58% of pyridine-N being directly converted into ammonium. Providing glucose as the extra carbon source, the degradation of pyridine was not affected, while the growth of the strain was promoted, and 41% of pyridine-N was converted into ammonium with a C/N ratio of 35. The ammonium was utilized rapidly by the strain, and a portion of it was transformed into nitrate, then to nitrite, and finally to dinitrogen if enough extra carbon was provided. Considering these characteristics, this strain may accomplish heterotrophic nitrification and aerobic denitrification simultaneously.     

Acetic acid production by Acetogenium kivui in continuous culture — kinetic studies and computer simulations

Summary This work considers the continuous production of acetic acid by the homoacetogenic and thermophilic bacterium Acetogenium kivui. A mathematical model for the growth kinetics has been developed. The unstructured model for growth and product formation includes product and substrate inhibition as well as maintenance energy effects. The associated model parameters have been identified by non-linear optimization and evidenced experimentally in continuous culture as steady-state data. By using a mineral medium with glucose as the energy and carbon source for the bacteria proper carbon balances are available. The model permits good predictions of steady-state concentrations. Offprint requests to: J. von Eysmondt     

Extracellular invertase of Rhizobium japonicum and its role in free sugar metabolism in the developing root nodules of Sesbania grandiflora

Extracellular invertase of Rhizobium japonicum and its role in free sugar metabolism in the developing root nodules of Sesbania grandiflora L. was studied. The enzyme hydrolysed sucrose extracellularly, and its release was substrate inducible. 0.1 Mβ-mercaptoethanol released the cell-bound form of this enzyme. The production of invertase was low when glucose, galactose, mannose, fructose and raffinose were used as carbon sources in the growth medium. In the developing nodules sucrose was the major sugar. The content of fructose was low in comparison with that of glucose – suggesting that in the nodules, fructose is converted to glucose prior to its entry into the bacterial cell. The content of glucose synchronised with the pattern of change in the activity of invertase in the nodules.     

Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O(2) uptake and CO(2) evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO(2) evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.     

Microflora of dissimilative nitrate reduction in a denitrifying reactor

The predominant denitrifiers and ammonifiers from methanogenic, aerobic and denitrifying reactor sludge were isolated and characterised. The population of ammonifiers increased by three orders of magnitude during the operation of the denitrifying reactor treating landfill leachate. The predominant ammonifiers were enterobacteria, and the predominant denitrifiers belonged to the genera Alcaligenes and Pseudomonas. Studies in pure culture showed that ammonia production by ammonifiers was favoured by fermentable substrates and by high C/N ratios. For acetate, only nitrite was obtained as the reduction product of nitrate, even at high C/N ratios. Furthermore, for glucose, nitrite addition caused a shift in fermentation products, with an increase in the acetate/ethanol ratio, with no significant differences in growth rates. Received: 14 January 1998 / Received revision: 11 May 1998 / Accepted: 21 May 1998     

Glucose metabolism in the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus.

Sulfolobus solfataricus is a thermophilic archaebacterium able to grow at 87 degrees C and pH 3.5 on glucose as sole carbon source. The organism metabolizes glucose by two main routes. The first route involves an ATP-dependent phosphorylation to give glucose 6-phosphate, which readily isomerizes to fructose 6-phosphate. In the second route, glucose is converted into gluconate by an NAD+-dependent dehydrogenation; gluconate is then dehydrated to 2-keto-3-deoxygluconate, which, in turn, is cleaved to pyruvate and glyceraldehyde. Each metabolic step has been tested in vitro at 70 degrees C on dialysed homogenates or partially purified fractions; minimal requirements of single enzymes have been evaluated. Identification of the intermediates is based on chromatographic, spectroscopic and/or synthetic evidence and on specific enzymic assays. The oxidative breakdown of glucose to pyruvate occurring in S. solfataricus differs from the Entner-Doudoroff pattern in that there is an absence of any phosphorylation step.